I would check your carb float level. Had similar symptoms on my 99 YZ. My dealer checked it - and adjusted it for free. If the carb float level is low, when you land from a jump it will bog. It may also cause other problems if way off. One other thing - Boyesen makes a float bowl that supposedly eliminates this, not sure if it works though, Saw it on the web site. Called Super Bowl I think.
I wouldn't mess with the 6 speed swap from a 99. A popular mod on a 99 was adding 2 teeth to the rear sprocket. Not sure if this is the case with an '03. Should be easy to find out.
Good luck